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Modular arrangement of proteins as inferred from analysis of homology
Author(s) -
Sonnhammer Erik L.L.,
Kahn Daniel
Publication year - 1994
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560030314
Subject(s) - computational biology , homology (biology) , protein domain , sequence alignment , protein superfamily , modular design , biology , pep group translocation , sequence analysis , domain (mathematical analysis) , sequence homology , genetics , protein sequencing , homology modeling , computer science , peptide sequence , phosphoenolpyruvate carboxykinase , dna , mathematics , programming language , gene , biochemistry , mathematical analysis , enzyme
The structure of many proteins consists of a combination of discrete modules that have been shuffled during evolution. Such modules can frequently be recognized from the analysis of homology. Here we present a systematic analysis of the modular organization of all sequenced proteins. To achieve this we have developed an automatic method to identify protein domains from sequence comparisons. Homologous domains can then be clustered into consistent families. The method was applied to all 21,098 nonfragment protein sequences in SWISS‐PROT 21.0, which was automatically reorganized into a comprehensive protein domain database, ProDom. We have constructed multiple sequence alignments for each domain family in ProDom, from which consensus sequences were generated. These nonredundant domain consensuses are useful for fast homology searches. Domain organization in ProDom is exemplified for proteins of the phosphoenolpyruvate: sugar phosphotransferase system (PEP:PTS) and for bacterial 2‐component regulators. We provide 2 examples of previously unrecognized domain arrangements discovered with the help of, ProDom.